New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
4 weeks
269
11
96418
5692
0
39
Parser of scientific names (...) !
Dmitry Mozzherin
9 weeks
19
3
53172
4107
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
11 weeks
6
2
43861
2200
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
6 weeks
21
6
40670
2961
0
6
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
14 months
14
11
40162
2003
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
5 months
2
...
31197
1569
Gadgets for bioinformatics (...)
Shintaro Katayama
2 years
1
26721
1888
0
0
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
16 months
14
1
26468
1477
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
11 weeks
25365
1955
Http requests to entrez e-utilities (...)
Jared Ning
3 months
4
...
25236
1175
A Ruby api for interacting with biomart services (...) !
Darren Oakley
4 years
18
5
23956
929
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
16 months
23814
1246
Create pretty svg-format images of features, gene models (...)
Dan MacLean
19 months
10
5
22147
1750
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
19619
902
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
19112
1131
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
16675
1047
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
16672
751
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
2 months
12
1
16298
1583
0
3
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
15833
961
A simple obo file handler (...) !
mjy
3 years
5
...
14595
669
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
7 months
12
3
12091
1244
A fast parser for fastq files (...)
Francesco Strozzi
3 years
10
...
11860
648
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
14 months
9
20
11760
805
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
14 months
8
5
11657
642
Data mining algorithms for jRuby (...)
arrigonialberto86
22 months
14
3
10642
957
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
9 weeks
2
1
9998
2231
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
9980
533
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9783
444
Low memory sequence emitters (...)
Pjotr Prins
14 months
8
1
9555
530
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
9245
377
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
12 months
3
...
9003
519
0
0
Ruby support for the baclava file format (...) !
Robert Haines
17 months
1
...
8950
529
Build genome output files (...)
Michael Barton
24 months
5
...
8759
353
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8490
354
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
8356
451
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
4 years
1
...
8298
319
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
2 years
5
...
8198
528
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
2 years
8
...
8043
340
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
8013
449
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
7996
343
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
16 months
...
7921
410
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7842
376
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7703
267
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
7190
273
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
7091
278
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
14
6856
267
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6464
264
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
6295
386
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
24 months
13
2
6153
522
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5805
277
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
5 months
4
3
5630
647
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5610
206
0
0
A plugin that allows you to parse large (...)
robsyme
4 years
1
...
5578
267
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
5470
350
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5371
256
Ruby binding for samtools tabix (...)
throwern
22 months
3
...
5188
345
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
5078
163
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
7 months
20
6
5026
803
Parser to work with file formats used in (...)
Ben J Woodcroft
6 months
...
5016
715
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4549
262
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
3 years
1
1
4510
275
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4483
272
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4457
253
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
5 months
...
4361
839
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4337
183
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4311
190
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
4089
185
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
4065
197
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
22 months
3960
350
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
8 weeks
3845
1334
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3765
171
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3667
249
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3599
172
0
0
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3586
265
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
23 months
1
...
3571
263
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3551
175
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
14 months
3
16
3254
545
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
3 years
1
...
3221
178
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3154
178
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
3065
187
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
17 months
1
...
2822
345
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
6 months
1
2694
486
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2608
567
0
2
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
9 months
1
2293
333
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2241
100
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2238
94
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2232
97
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2136
83
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
18 months
6
...
2130
114
Biostars data-mining and statistical analysis (...)
Joachim Baran
16 months
2102
276
Gggenome Ruby client (...)
Mitsuteru Nakao
24 months
1
...
2071
171
Ruby ensembl rest api (...)
Alberto Donizetti
22 months
3
...
1994
181
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
1980
94
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1943
86
Generalized linear models for statsample (...)
Ankur Goel
22 months
1941
178
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1937
89
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1930
93
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1912
91
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
4 years
1
...
1903
65
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1896
88
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1890
95
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1869
101
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1854
91
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1824
93
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1817
94
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 years
1
1
1731
94
Specimens quickly extracted and digitized, or just "squid" (...) alpha
Matt Yoder, Rich Flood
7 weeks
...
1707
1707
0
25
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
18 months
...
1704
184
Interface for express beta diversity (...)
Ben J. Woodcroft
18 months
...
1683
187
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1666
244
Bio-repeatmasker (...)
Andrei Rozanski
19 months
1642
175
Build graph with jRuby (...)
Matteo Picciolini
2 years
1631
94
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
3
...
1627
92
A parser for cigar format alignments (...)
Ben J Woodcroft
17 months
4
...
1545
190
Web server for bio-samtools (...)
homonecloco
14 months
...
1395
188
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1373
91
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
9 months
1178
182
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
2 years
2
...
1169
97
0
0
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
90
1
1144
424
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
2 years
...
1102
97
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
1 day
...
1078
1078
Helper methods for reading .delta files (...)
robsyme
4 months
...
898
318
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
7 months
1
...
879
193
0
0
Mine publications for gene names (...)
Pjotr Prins
17 months
...
771
92
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
17 months
677
76
A web app wrapper for genevalidator (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
1 day
...
630
630
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
12 months
1
...
627
98
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
10 months
...
592
106
Tools to work with fasta files, indexed with (...)
homonecloco
10 months
...
547
99
0
0
Tools to manipulate blat files from the command (...)
homonecloco
10 months
...
533
98
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
8 months
...
491
102
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
8 months
...
490
100
The api for freebayes version #{bio::freebayes::extversion} (...)
Natapol Pornputtapong
10 weeks
466
434
Aggregate fastqc (quality control for next generation sequencing (...)
Raoul Jean Pierre Bonnal
5 weeks
...
464
273
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
434
62
(...) pre
pre
427
12
Api of picard tool (...)
Natapol Pornputtapong
10 weeks
351
227
A pipeline manager (...)
Francesco Strozzi
4 months
11
10
303
125
0
0
(...) pre
pre
185
16
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-08-04
**) number of commits on GitHub (last 7 days & last 90 days)